def generate_slab_phantom(size,
voxelsize,
iso,
slab_defs,
phantom_name='slab'):
"""Args:
slab_defs ([(int, material), ...]: define thickness and material of each slice in slab phantom
"""
os.makedirs(OUTPUT_DIR, exist_ok=True)
dens = np.empty(np.product(size))
# write Monte Carlo geo.txt file
center = list(iso)
center[2] += (voxelsize[2] * size[2] / 2.)
print("Generatring %s slab phantom:" % phantom_name)
print(" Isocenter is at %s" % str(center))
print(" Phantom size in voxel is %s" % str(size))
with open(
os.path.join(OUTPUT_DIR, "mcgeo_{!s}.txt").format(phantom_name),
'w') as fd:
fd.write("{:d} {:d} {:d}\n".format(*size))
fd.write("{:f} {:f} {:f}\n".format(*voxelsize))
fd.write("{:f} {:f} {:f}\n".format(*center))
# ZYX ORDERING
idx = 0
for layer in slab_defs:
for ii in range(np.prod([layer[0], *size[:2]])):
dens[idx] = layer[1][0]
fd.write("{:f} {:d} {:d} {:f}\n".format(*layer[1]))
idx += 1
# write dosecalc ready phantom file and fmaps file
# vol = Volume.CenterAt(dens.astype('f').reshape(size[::-1]), np.divide(center, 10), np.divide(voxelsize, 10))
dens = dens.reshape(size[::-1])
dens = np.concatenate([np.zeros((4, size[1], size[0])), dens], axis=0)
vol = Volume.CenterAt(
np.ascontiguousarray(np.transpose(dens.astype('f'), (1, 0, 2))),
(0, voxelsize[1] * (dens.shape[1] - 4) / 20, 0),
np.divide(voxelsize, 10))
print(" Data written to file is of size %s" % str(vol.data.shape))
vol.generate(
os.path.join(OUTPUT_DIR, 'phantom_{!s}.h5'.format(phantom_name)))
fmaps = Fmaps()
fmap_wts = np.ones((10, 10))
# fmaps.addBeam(Beam(fmap_wts, gantry_deg=-90, couch_deg=90, coll_deg=0, iso=np.divide(iso, 10), sad=100, beamlet_size=(0.5, 0.5)))
fmaps.addBeam(
Beam(fmap_wts,
gantry_deg=0,
couch_deg=0,
coll_deg=0,
iso=np.divide(iso, 10),
sad=100,
beamlet_size=(0.5, 0.5)))
fmaps.generate(
os.path.join(OUTPUT_DIR, 'fmaps_{!s}.h5'.format(phantom_name)))
